Project Crimson
by FallenAngelsRevenge
Summary: We all know that Miranda saved Shepard's life with Project Lazarus, but what if that wasn't the only project she worked on? What if Shepard wasn't the only person she saved? A Cerberus vessel detects an energy spike on an unknown planet and 'Project Crimson' is born... Naruto/Tali, possibly more
1. Recovery

~A/N: Hey, got a new story here, this one's a Naruto/Mass Effect Crossover, making me the 39th one on the site! :D I recently bought ME3 and this idea wouldn't stop hounding me until I typed it out. I don't believe this kind of thing has been done before (at least, in terms of getting Naruto into the ME universe), so we'll see how it goes.

Also, don't spoil anything from ME3 for me! I started another ME2 run because ME3 pretty much sucks unless you import . so no spoilers!

~One And Only Disclaimer of the Story: I own neither Naruto nor Mass Effect. They are owned by Kishimoto and Bioware respectively.

~Project Crimson~

~A Naruto/Mass Effect Crossover~

~Chapter 1: Recovery~

Naruto painfully staggered away from the crater that had been made only minutes before, dust that had been thrown hundreds of feet into the air just beginning to settle around him. His skin was blackened, he could both feel and hear it crackling like paper every time he moved. Nearly every nerve in his body screamed at him to stop, to lie down, to just close his eyes and let sleep overcome him.

And despite all of that, he couldn't have been happier. Madara had finally been defeated. Their final showdown had been long and brutal. It had decimated nearly everything within several miles of the epicenter. But Naruto had come out on top in the end. It would cost Naruto his life, but as long as nobody else had to give their lives fighting a madman's war Naruto was happy.

After almost a minute of agonizing stumbling, Naruto finally staggered enough that he lost balance and fell backwards into the dirt, the impact causing too much pain for him to even bother attempting to stand back up.

He stared at the sky, darkened by the floating dust and debris in the air for several minutes, and briefly wondered if there was a place for him out there. Where did shinobi go when they died? He supposed he would find out in just a few minutes.

Naruto lay there in the dust and accepted his fate, closing his eyes just as a shadow enveloped his figure. He couldn't be bothered to open his eyes again, but he heard muffled shouting and then a faint stinging sensation before the bliss of unconsciousness descended upon him.

~~PC~~

The Illusive Man was not the kind of person who could be easily surprised. His information network was more extensive than even the infamous Shadow Broker's. As a result, there were not many things that he didn't know of or at the very least expect.

That being said, when one of his lower-ranking officers informed him of an exceedingly large energy spike on a fairly unknown planet on the rim of the galaxy, he was intrigued.

"Exactly how large is this energy spike if it warrants contacting me directly?" The Illusive Man questioned through his communications channel.

"Sir, the men who picked it up on sensors told me it was the highest spike they'd ever seen. They said it was nearly off of the charts." The unnamed officer responded.

The Illusive Man raised an eyebrow—not that the man he was speaking with could see it. "Have they ascertained the source of the anomaly?" He questioned the officer again.

"Yes, sir, they've taken the liberty of acquiring it before contacting you," The man began somewhat uncertainly. It was for good reason; the Illusive Man – or at least a high-ranking officer – was generally contacted before any major decisions were made on how to proceed. 'Taking the liberty' of doing something potentially disastrous before it was relayed through a higher-up usually ended in unemployment for the guilty—which often ended in death.

"Sir…" The officer continued, unsure. "The source was a living creature – a human, from what the soldiers told me – and they say he's in very bad condition, unconscious but still alive. They've used as much medi-gel as will help, but the medic stationed on the cruiser says he's practically been burned to a crisp and he'll only last for a few days maximum. They're requesting that something be done." He finished.

The Illusive Man could tell that the officer was nervous.

"Send me the records of the energy spike." Was all he said in response.

"Yes sir, right away." The officer went silent for several moments, then the Illusive Man's omni-tool chimed and a small holographic display appeared with the records of the anomaly in question. The Illusive Man's eyes actually widened a fraction at the display.

"Are you sure these are the correct records?" He inquired.

"Yes, sir."

"Hmmmm… Remarkable," The Illusive Man mumbled more to himself than to the officer he was speaking with. "I will send someone over to retrieve him as soon as possible, please inform the soldiers who found him and tell them someone will arrive within the next day." He finished.

"Yes sir!" With that, the officer sent him the coordinates of the soldiers' current location in orbit around the planet the anomaly was found on and ended the connection.

The Illusive Man quickly initiated a hailing frequency, getting a response almost immediately. A hologram of a dark-haired woman in skintight clothing appeared.

"Yes, sir?"

"Miranda, how is Commander Shepard's progress at the moment?" He questioned.

"Well, it's slow going, though we are making steady progress sir. But you already know that. It _has_ been over a year since we recovered her." She stated with a raised eyebrow.

"Indeed," He responded. "Would you be able to leave Shepard for several days, possibly weeks?"

"Yes, sir, if I put Wilson in charge I could be absent for some time, though progress would be slower while I'm absent." She responded with a questioning tone.

"Good, I'd like you to investigate something that a few of my men have found on a planet near the rim of the galaxy. They investigated an energy spike and found the source to be what they say is a human. From what I've gathered, his state is very similar to the state Shepard was in when we recovered him." He said with a hint of finality.

"Sir?" Miranda questioned, somewhat shocked.

"I want you to go and retrieve him from the soldiers and stabilize him like you did Shepard. From the energy readings, he is quite possibly the most powerful biotic in the galaxy, and we may be able to learn something from him. I'd like you to leave within the next few hours. I'm sending you the coordinates now."

"Yes, sir." And with Miranda's response, the Illusive Man ended the transmission. He would not have Miranda work on the 'human' they had found for too long – Shepard was still the top priority – but it would be interesting to see how things played out. Perhaps this newfound creature could be of some use.

~~PC~~

Miranda sighed as her shuttle docked with the small cruiser the soldiers were stationed on. The Illusive Man was sending her out on an assignment that could take days or even weeks? That time could be better spent on Shepard!

However, it wasn't Miranda's place to disobey the Illusive Man's orders. The most she could do was get this fiasco over with as quickly and efficiently as possible.

The airlock hissed as her shuttle docked with the larger spacecraft and she sighed once again as she stepped through the parting doors and onto the craft, causing several soldiers in the immediate vicinity to begin eyeing her like a piece of meat.

One of the crew members – a female human – rolled her eyes with a hint of disgust and stepped forward.

"Miranda Lawson?" She inquired. Miranda nodded in confirmation. "Come with me. You'll probably want to see this." The crew member finished as she began leading Miranda through the corridors.

"We found him on the surface," She began informing Miranda as they strode through the halls and into an elevator. "A few soldiers were sent down to investigate an extremely large energy spike and he was the source. Though the condition they found him in was… well, it wasn't pretty. I've done what I can to stabilize him, but the equipment on this ship isn't advanced enough and he's slowly degenerating," She said as they exited the elevator and made their way through several more halls. "Frankly, I have no idea how he's still breathing." She finished as they entered the room were the 'anomaly' was kept.

Miranda was quite simply surprised—for three reasons, actually. The first – and less important – was that she had been expecting the crew to be exaggerating a little, or that things weren't as bad as they had made them out to be.

In reality, they were much worse.

The boy – for that was what he looked like, though she couldn't tell exactly – had quite literally been burned to a crisp. His skin was blackened, and it was peeling in some places as well. The majority of his hair had been burned off, with blackened and mangled patches here and there along his scalp, and on some parts of his body his skin had been incinerated off completely and the blackened and burnt muscle underneath was showing. She honestly didn't know if he was in better or worse condition than Shepard was when they found her. At least Shepard had been wearing armor.

The second was that the boy _was_ a human. She had seen the energy readings, since the Illusive Man had sent them to her before her departure, and she had refused to believe that the source of the spike was a human. However, the boy lying on a table nearly burnt to a crisp in front of her was undoubtedly human.

That being said, the energy spike was over seven times greater than the highest energy readings that Miranda herself had managed. The only possible explanation was that whatever the boy had done had been so powerful that it resulted in his current state.

The third reason was also the simplest. He was still alive and breathing, although it was definitely labored and very shallow. Miranda was amazed at the boy's sheer will to live. She was fairly sure that by the time Shepard was at this stage, he had already been dead.

She sighed again.

"Okay, I'll take him and see what I can do. Thank you for your help." She said in dismissal of the female crew member. Several Cerberus soldiers filed into the room and aided Miranda in preparing the gravely wounded boy for transfer from the cruiser to her shuttle.

She resisted the urge to slam several soldiers against the wall with her biotics for allowing their eyes to wander as they made their way back onto the shuttle with the injured boy in tow. Sometimes she hated her father for making her 'perfect'.

As she disembarked from her shuttle and stepped back onto her starship, she ordered the navigator to enter the coordinates that the Illusive Man had recently given her. He wanted the boy placed in a station on the rim of the galaxy, as he didn't want anybody else picking up energy spikes from the boy. He was to be placed in a station similar to the one Shepard was currently occupying – though on a smaller scale – and was to undergo almost the same treatment as well. The Illusive Man had dubbed it 'Project Crimson'.

Miranda moved the boy to the ship's med-bay as quickly as possible and immediately began attempting to get the boy stabilized at the very least. The chief of medical staff on the starship assisted her in getting the boy situated for the several-hour long trip to their destination. Miranda started with an initial scan, hoping beyond hope that severe burns were the extent of the boy's injuries and there was little if any internal damage.

Unfortunately for the both of them, nearly half of the bones in his body had been damaged in some way, and some of the muscle tissue and ligaments had been torn beyond a human's natural healing ability. Several of his organs had been bruised as well, and many of the blood vessels and veins in his limbs had been severed or severely bruised, likely due to harsh impacts in those areas.

Miranda groaned and resisted the urge to repeatedly bash her head into the nearest solid object. This boy was going to take a _lot_ longer than a mere week to stabilize.

Miranda suppressed those thoughts and began focusing instead on stabilizing the boy as quickly as possible. She fired up her biotic amplifiers and organized her medical tools.

It was time to get to work.

~~PC~~

Miranda once again entered her private quarters on the station that was her temporary home, striding immediately into the bathroom. She removed her skintight clothing and barely spared the reflection of her 'perfect' body in the mirror a second glance as she entered the shower and turned the hot water on.

Sure, there were decontamination stations placed throughout the station that removed the need for bathing as long as you took a walk every so often, but she enjoyed showering more because of the feel of the water cascading down her body. Decontamination just didn't make her feel as clean as showering did.

It had been just over a week and a half since she had arrived at the station with the mysterious young man, and she had just that morning managed to get him stabilized. Now that he didn't require constant medical attention from either her or her assistant, she could get a good nights rest and relax a little bit before diving back into her work.

The boy was… remarkable, to say the least. Compared to Shepard, this project was much more interesting. Bringing Shepard back from the dead had been an amazing feat, that much was true, but after she was revived and the correct implants were in place it was pretty much a waiting game. All they could do was observe her condition and monitor her progress, perhaps altering a few things here and there.

However, this young man the Cerberus soldiers had found on a rim planet… he was far from a normal human. She was beginning to have doubts that he was human at all.

When she had done another scan on him upon his arrival and situation into the station, it had been revealed that several of his bones were either partially or completely repaired—with no outside help whatsoever. Hell, one of his ribs that had nearly been snapped in half only a few hours before was now as good as new! Several of the bones in his hands and feet had also mended themselves—they were small bones, with minor fractures and breaks, but they still shouldn't have healed so fast.

She had dismissed it as something that the medic on the soldiers' cruiser had managed to accomplish, whether it was intended or just luck she couldn't be sure. However, over the next few days, she began noticing the same thing—and it wasn't just the bones that were 'miraculously' healing either. Some of his internal organs' conditions had improved by leaps and bounds in only a few short days. A non-fatal yet still extremely problematic rupture in his intestinal tract had healed itself completely in less than a day!

Over the first several days, she had bounced back and forth between helping to stabilize the boy and determining what the _hell_ was causing such amazing regeneration. Near the end of the fifth day, she had done several scans and a few had managed to pick up a unique energy signature coming off of the boy like a blanket.

Acting on a hunch, she had one of the technicians stationed near the lab do a cross-check of the readings of both the new energy signature and the signature of the energy spike that led Cerberus to the boy in the first place.

The next morning, the technician had approached with some astonishing news. According to the readings and the cross-check, behind the initial biotic signature of the energy spike, there was another energy signature that matched this one, as well as a third signature that was slightly weaker than the other two.

Throughout the next few days, Miranda performed several dozen more thorough scans of the young man and found confirmation that the boy had _three_ different energy signatures. One matched the signature of biotic energy, but the other two were complete unknowns—though they were remarkably similar to each other.

She managed to piece together through both scans and observation that one of the unknown signatures – the stronger one – was what was healing the boy. After acquiring that information, she focused her medical efforts on the large bone fractures, as well as organ damage, leaving this 'healing energy' to work on the less serious injuries.

The morning of the eleventh day, she and her chief assistant had declared him stable. He wouldn't heal by himself – or at least, if he did, even with his remarkable healing it would take many years to accomplish – but he wouldn't die due to his injuries.

They had spent the rest of that day discerning the best and most prominent areas to place several kinds of implants. Most notable were the neural implants – which would revive any nerve tissue that had been damaged – and skeletal implants, which would strengthen his skeletal structure, as well as aiding in the reforming of damaged bones.

The young man was certainly intriguing. Miranda was actually tempted to request to be reassigned to the boy's medical staff instead of Shepard's, but she knew the Illusive Man would never grant that request. After all, Shepard was an irreplaceable icon to humanity.

Turning off the water and stepping out of the shower to dry herself, Miranda merely slipped on some undergarments before crawling into bed. The Illusive Man had assigned her to the boy for 'three to four weeks, depending on his condition', and she was going to stay here for as long as she could—especially if the boy had any more surprises in store.

~~PC~~

"Miranda Lawson?"

"Yes. You're Doctor Joseph Kelaar, I assume?"

"You would be correct in that assumption, Miss Lawson."

The man – Doctor Joseph Kelaar – stepped out of the airlock and into the station where Project Crimson was based, briefly shaking hands with Miranda. She gestured for him to follow her and led him though the space station to the medical room the young man was situated in. It was a quiet journey, neither of them initiating a conversation. As they entered the room, several automated arms finalized the integration of the neural and skeletal implants into the boy's systems.

"This is the boy you have sent me the information on?" The man asked. He was a fairly young human male, as well as tall, with dark brown hair fashioned into a short ponytail. Doctor Kelaar was one of the best medical personal Cerberus had to offer – other than Miranda – and he would be taking over care of the boy while Miranda went back to oversee Shepard's progress once again.

"That's correct. He's been a very… surprising patient, to say the least." She responded. She was actually kind of disappointed. She didn't _want_ to go back to overseeing Shepard at this point, the young man before her was just too amazing. Every week they found something new and completely unknown related to the boy. While he was certainly human, he was definitely not an ordinary one. He had more biotic power than most asari for christ's sake!

Compared to him, Shepard would be boring as hell. However, Miranda would not go against the Illusive Man's wishes. If he wanted her to return to Project Lazarus, she would do so.

"Yes… I must say, the information you have sent me so far has been… strange. I find it kind of hard to believe." He said with a playful smirk.

"I found it hard to believe as well, until I saw it with my own eyes. Just be prepared for the unexpected with him, he's given the medical staff several surprises already." She responded.

"Well, I'll leave him in your care then," Miranda continued. "I've already packed my belongings, so I'll be leaving shortly." She said, moving past the doctor and towards the door.

"Have a pleasant trip…" He said, gazing at the boy with a glint in his eyes that Miranda didn't fail to miss. It looked like eagerness, but there was something else in there, too… Oh well, it wasn't Miranda's job to care for him anymore, the priority now was getting back to Shepard.

She quickly boarded the shuttle, taking it back to her starship and beginning her journey back to the station where Project Lazarus was based.

Miranda just couldn't shake this feeling she had… something about that boy was important. She just knew it.

~~PC~~

"Where would you like to start, Doctor Kelaar?" The chief medical assistant – a young blonde woman – questioned the new medical head.

The man glanced once again as his datapads, mulling over several thoughts before deciding.

"I think I'll take this first day to settle in and get used to the station, Miss Addler. We'll begin getting him back to full health first thing tomorrow."

"Of course, sir." She responded, before striding out of the room to inform the rest of the medical staff.

Doctor Kelaar sauntered up to the unconscious boy.

"Yes, my boy, first thing we need to do it get you back to full health," He began. "Then we may begin the testing…"

~~PC~~

~A/N: Well, here it is. This is more of a 'Prolouge' than a first chapter, but eh, whatever. Reviews are always appreciated and help motivate me to write more, so click the button!

Also (for those that have been wondering), the reason that I haven't updated my other two fics for a while (or uploaded another that already has the first few chapters typed up) is because the flash drive that I use to store all of my fics on is gone. I left it at school on the last day because my final was on it and I forgot it in the computer w stupid me… Anyways, while I'm in the process of getting it back, I won't be able to update any of the other stories until I have it, as I don't feel like typing another few thousand words for each story =3 I should have it in a few days though, so hopefully I'll update soon! (Though I may get obsessed with this one and slam out a few chapters before I do anything else X3

_**Original Post ~ 6/28/2012 ~ 3,655 words**_

_**Edited Post ~ 7/22/2012 ~ 3,905 words**_


	2. Awakening

~A/N: First off, thanks to Brian Stentzel for catching the whole 'referring to Shepard as "him"' thing. I actually meant for Shepard to be female (Sorry if a few are disappointed), but I play as a male Shepard when I play the game, so I guess it's a habit to write like Shepard is a male, and I may make the same mistake later on, so you'll have to forgive me. I'm re-uploading the first chapter with the fixes, so if it REALLY matters then you can reread it.

I'm not going to give a detailed description of Commander Shepard, primarily because people will have different appearances in mind anyway, so I'll just say I pictured the default appearance from ME3 when making the fic. If you're curious, find it on Google Images.

Also, since several of you seem to expect me to abandon this after just a few chapters (which is warranted, since 90% of the fics on this site are like that =/) I will not abandon _any_ fics. Even "A Fallen Angel" – which I haven't updated in around 6 months – is not abandoned; I have the next chapter half written on my lost flash drive, and will continue the story once I get it back.

Frankly, I'm surprised by how popular this story is with only a few thousand words O.o it has more reviews, follows/alerts, and favorites than many 20k+ stories out there, so I guess I'm doing something right! Hopefully this chapter doesn't disappoint.

_Blacken the cursed sun.  
You're not the only one,  
To have sunk so far and low.  
There is no tomorrow._

_Blacken the cursed sun,  
Blacken what's yet to be done,  
Blacken because now you know,  
There is no tomorrow!_

_Blacken the Cursed Sun ~ Lamb of God_

~Project Crimson~

~A Naruto/Mass Effect Crossover~

~Chapter 2: Awakening~

Commander Jane Shepard stepped off of the shuttle and dropped the small distance to the metal floor of the Normandy with a satisfying thud, followed by Garrus Vakarian, Kasumi Goto, and the Normandy's newest crewmember—Tali'Zorah nar Rayya. They had just gotten back from the surface of the planet Haestrom, after battling through piles of geth troopers and even a hulking Colossus to get to said quarian.

Shepard approached the armor locker and removed her battle armor—though she was the only one of the four who did, since Kasumi never wore armor in the first place, Garrus never took _off_ his armor, and Tali couldn't take off her armor for fear of contracting a lethal disease.

The foursome entered the elevator in silence and both Garrus and Kasumi left on the third level of the Normandy, the level that held the crew's quarters and their preferred places of lodging. Tali and Shepard made their way to the Communications Room after arriving on the CIC level.

When they entered, Jacob was waiting to 'greet' the new recruit—as he and Miranda did frequently. He gave the quarian a warm reception and welcomed her and her skills to the ship.

The same could not be said of the quarian herself.

Tali blatantly told Jacob that she didn't trust him – or anyone on the ship who was loyal to Cerberus – and that she was not working for Cerberus, she was working with Shepard—who was in turn working _with_ Cerberus. That was the only reason she had even agreed to board the ship. Jacob seemed a little put out by this, but also seemed determined to show her that Cerberus wasn't so bad.

Shepard interrupted the two before Tali could really get started on her distrust of Cerberus and proceeded to get her situated on the engineering level, working with the engines.

Not even ten seconds after she had gotten back into the CIC, yeoman Kelly Chambers flagged her down.

"Commander Shepard, the Illusive Man wishes to speak with you in the Comms Room."

'_Damn… I can already tell this is going to be trouble.'_

Shepard made her way once again to the Communications/Briefing Room that had now been vacated and activated the holographic communications display, lowering the table that occupied the center of the room into the floor.

She stepped into the space previously occupied by the table and a cylindrical field materialized around her, changing the environment and providing her with an image of the Illusive Man.

"Ah, Shepard," He began, as if her contacting him was unexpected. "How did your mission on Haestrom go?"

"It was alright. We successfully recruited Tali and managed to keep a quarian marine alive. I was told you wanted to see me?" She responded.

"Yes, about that…" He said, before taking a drag of his cigarette. He blew the smoke out slowly, and Shepard was somewhat tempted to just tell him to spit it out—both the cigarette and the information. "It appears that something has… come up on one of our stations near the rim of the galaxy. I'd like you to check it out."

Shepard raised an eyebrow. "Is that all you're going to give me? I'm going to need more information than that if you want me to investigate." Shepard said with crossed arms.

"Of course, Shepard." He responded. "I wouldn't expect you to go in completely blind. The station is located in the Frolus Nebula on the rim of the galaxy near the Shrike Abyssal. A little under a year ago Cerberus funded 'Project Crimson', a project near identical to your own," This earned a somewhat shocked look from Shepard. "The subject was a boy found on an unexplored planet due to an energy spike that was sensed by a nearby Cerberus vessel. He was in very bad condition."

"So then what's the problem?" Shepard asked. She had a feeling that this wasn't going to be a simple mission by any means.

"A couple days ago, the station went dark. All communications to and from the station stopped and the reconnaissance team I sent in never reported back. I'd like you to investigate what happened and recover any survivors." The Illusive Man stopped and took a drink of some kind of alcohol from a glass on his desk.

"Survivors? So you think the station has been attacked?" Shepard questioned.

"I can't be sure. Either way, something happened to the station, and I want you to figure out what it was." The Illusive Man responded bluntly.

"So what's in this for me? Or are you asking for a favor?" Shepard said with a slight scoff.

"I don't call in favors, Shepard, I don't need to," The Illusive Man responded with no small amount of both arrogance and pride. "Tell me, Shepard, you have seen Miranda's biotics in action, correct?"

"Of course, why?" Shepard asked, somewhat exasperated.

"How would you say Jack compares to Miranda in terms of biotic power?" The Illusive Man continued, blatantly ignoring Shepard's previous question.

"I'd say Jack is almost twice as powerful as Miranda when she needs to be, what does that have to do with anything?" Shepard questioned. She was starting to get annoyed.

"The energy readings we got from the boy were over seven times greater than Miranda's highest biotic energy output on Cerberus record," The Illusive Man said. Shepard's eyes widened. Over seven times more powerful than Miranda? "And since then, there have been several more power spikes. The latest one was almost twice as powerful as the original." Shepard was somewhat speechless at that. A biotic who was more than fourteen times more powerful than Miranda? That was seven times more powerful than Jack!

"Where is this heading?" She managed to say after a few moments of regaining her composure.

"When you investigate the station, I'd like you to see what has become of this boy, whether he is alive or not. If he is alive and conscious, you may attempt to recruit him for your mission. I'm sure he would be a valuable asset to your team."

"And if he's not alive?"

"Then I have wasted my funding and will not make the same mistake again." The Illusive Man said coldly.

"Can you tell me more about this 'Project Crimson'?" Shepard questioned.

"I can't tell you many of the details, but if you really want to know, ask Miranda. She was the head of medical staff for the first month or so of the project." The Illusive Man replied, causing Shepard to furrow her eyebrows. She'd have to question Miranda about it.

There were several moments of silence as Shepard thought things over. A biotic that was seven times more powerful than Jack? It was an extremely good opportunity to add some firepower to her makeshift team. However, nearly nothing was known of the situation, so they were practically going in blind.

"I'll investigate this station of yours and find out what happened. If what you say is true, this boy could be a good addition to the team." She eventually said.

"Good." The Illusive Man said sharply. Of course, he had already known that Shepard would accept, otherwise he wouldn't have even asked. "I ask you to investigate as soon as possible, I have a lot of funds going towards Project Crimson and I'd like to know if continuing the project is a waste of time and money. Good luck, Shepard."

And with that, the Illusive Man ended the connection.

"I wouldn't need luck if you'd give me more than just the damn location…" Shepard mumbled to herself. She tended to get a little more aggressive whenever the Illusive Man was concerned. For that matter, half of the crew tended to be more aggressive when the Illusive Man had a mission for them.

Shepard sighed. The Illusive Man had told her to 'investigate as soon as possible', which – in Illusive Man lingo – meant 'investigate right the hell now'.

Shepard left the Briefing Room and once again entered the CIC, entering the coordinates the Illusive Man had just sent her.

"Coordinates locked, Commander Shepard. The Normandy will arrive in just over four hours." EDI stated through the ship's loudspeakers.

"Thank you, EDI." Shepard responded simply.

The Normandy banked and began its voyage to the Frolus Nebula while Shepard entered the elevator once more. If it would take several hours to get there, she would speak with Miranda about 'Project Crimson.

She exited the elevator on the third floor and made her way to Miranda's office. Said woman looked up as Shepard entered, and they exchanged greetings.

"I've got some questions, Miranda." Shepard stated, getting straight to the reason she was there.

"Oh? What about?" Miranda asked.

"I've just come from a talk with the Illusive Man. He's given the team a mission and he said you could give me a little more info." Shepard said in response to the woman's questioning.

"Now why would he say that?" Miranda replied with a questioning tone.

"He mentioned something about a 'Project Crimson'," Shepard said, earning a furrowed brow from the black-haired officer. "Said something about you being head of medical staff for a while."

"I must say, Shepard, I'm curious as to what the mission is about now, if he gave you that information."

"The station where Project Crimson was based has gone dark—no communications coming out. The Illusive Man wants us to investigate what happened. We're going in practically blind, so I asked him for some info on Project Crimson, and he told me to ask _you_ for the details." Shepard said with an expectant look.

"Well, I can't tell you very much about the station itself; my memory is be a little hazy. I was only there for about a month, and that was almost a year ago." She said.

"I'll take what I can get." Shepard replied with a shrug.

"Well, Project Crimson started when a Cerberus vessel picked up an energy spike originating from a planet near the rim of the galaxy, in an uncharted solar system. When they found the source, they brought it back and contacted the Illusive Man, who sent me to check it out." Miranda began.

"The source turned out to be a human—a young man. He was in horrid condition, almost as bad as you were when we found you. The only difference was that he was still alive, just unconscious," This earned a surprised look from Shepard. "I transported him to the station and over the course of a month stabilized him and began placing implants into his system. He was… surprising. Enhanced regeneration, _extremely_ high biotic potential, and _three_ different sources of energy, one biotic, the other two unknown. He just kept surprising the medical staff. That's all I can really tell you. Someone else took over the project after that and I returned to Project Lazarus."

"Can you tell me how many armed personnel there were?"

"As far as I can remember, there was virtually no armed guard. It's been a while, though, so that's probably changed."

"Well, thank you for the information anyway. The Illusive Man says that if the boy's alive and conscious, we can try to recruit him." Shepard said.

"Really? Well, don't get your hopes up," She responded with a slight grimace. "We have no idea who he is and I haven't heard anything about him from Cerberus. Chances are, he's not even conscious yet—if he's even alive at all."

"Well, we can always hope," Shepard replied with a solemn nod. "He'd be a good addition to the team with how powerful his biotics are."

Shepard left Miranda's office and went to the armory. Might as well spend the next few hours making sure she was ready for anything.

~~PC~~

Shepard exited the shuttle and moved into the airlock of the Cerberus station. She readied her battle rifle as Tali, Jack, and Miranda moved into the airlock as well and brought their weapons to bear. The door in front of them hissed and they stormed through as it opened, ready for an ambush or a surprise attack.

What they got was a security checkpoint that doubled as a waiting room and a very surprised security guard/receptionist who now feared for his life.

"W-what? Who are you?" He managed to stutter out, before raising his hands into the air to show he was unarmed.

"I'm Commander Shepard. I've been sent by the Illusive Man to investigate the lack of communications from this station. You wouldn't happen to know anything about that, would you?" Shepard responded without lowering her weapon.

The guard seemed to relax a little. "Oh… in that case, I'll call Doctor Kelaar down here. He should be able to explain things." The man said, seemingly waiting for permission.

Shepard gave him a nod – a sign that she wouldn't blow his brains out for contacting someone – and he used a short-range communicator on his omni-tool to call this 'Doctor Kelaar' down to their level.

A few minutes passed in tense silence as they waited. Eventually, the far door hissed open and a fairly tall man with a brown ponytail stepped into the room followed by two armored guards.

'_Armored security personnel?'_

"Ah, Commander Shepard," The man began. "Adams told me you're here to investigate the lack of communications from the station?" He finished with a questioning tone.

"Yeah, the Illusive Man sent us to investigate when his recon team never reported back." Shepard confirmed.

"He also wants us to check up on Project Crimson." Miranda added quickly.

The doctor gave her a look that almost seemed hostile, but wasn't quite. He seemed to give the team an appraising look, before nodding and gesturing with his hand.

"Very well then. If you would follow me, I'll take you to the medical centers and explain the situation on the way." He said, not waiting for a response before moving to leave the room.

Shepard and her team looked at each other, Shepard with a raised eyebrow and the others with shrugs, before reluctantly following the doctor further into the station. He was their only source of information right now and they needed to figure out what was going on. They lowered their weapons, but didn't holster them completely.

Shepard and her team grew more on edge as they moved deeper into the station. Nearly every room they moved through had at least one armed guard in it. And they weren't regular security guards either, they were wearing full body armor – complete with helmets – and each wielded an assault rifle. There were very few civilians milling about as well.

"The comms have been on the fritz for a few days now, so we've had to resort to using short-range communications until we can get them back up again. That's why the station's gone dark and it's also why you weren't hailed when you docked." Kelaar began as they weaved through the corridors, passing several scientists who gave them wary eyes; sometimes Shepard caught a hint of fear in them.

Well, that certainly explained the lack of communications, as well as why the security guard had used an omni-tool to contact the doctor instead of the station's own PDA system.

"So what about the recon team the Illusive Man sent in?" Shepard questioned as they entered an elevator.

"I've heard nothing of a recon team entering the station…" Kelaar responded. The elevator doors opened and they began winding through the halls again. "I can't be sure what happened to them, but they never made it to the station, I can tell you that."

They finally entered a fairly large room that held several lab tables, as well as some desks and various medical tools. Six guards were stationed around the room—one in each corner and one on either side of the door they had just come though, which happened to be the only door in the room. Kelaar lead them into the middle of the room before turning to face them. Shepard immediately felt the tension in the air.

"So how has Project Crimson been going, Doctor Kelaar?" Miranda questioned before Doctor Kelaar could speak.

"Oh, it's very interesting, Miss Lawson," He responded with enthusiasm. "The subject is extremely… surprising, to say the least. I—" At this point the door hissed open and a scientist came rushing into the room.

"Doctor Kelaar, Subject Crimson is—" The man stopped as he realized that Shepard and his team were occupying the room as well. "…something's come up." He stated urgently, giving the doctor a look.

"Hmmm, yes, well," Kelaar said quickly. "Your mission will have to wait, Commander Shepard. It appears that duty calls." With a nod of his head, Kelaar moved towards the door.

Before leaving, he put his hand on one of the guards' shoulders. He nodded and the guard gave a nod in return, before the doctor disappeared behind the closing doors.

There was a tense silence.

"Ready your weapons," Shepard said quietly to her three allies. "I have a bad feeling about this…"

Several moments passed.

One of the guards made a movement, causing the rest to bring their weapons to bear. Shepard and her team did so as well, each picking a target.

The tension was palpable. It was a standoff. But what the _hell_ was going on?

"What the hell's going on here? Aren't you supposed to be our allies?" Jack voiced Shepard's thoughts perfectly.

Shepard's helmet chimed as a connection with the Normandy was established.

"Commander," Came EDI's voice. "I have scanned the station. The Communication's Relay is online and undamaged."

By the looks of Miranda's grimace, the others had heard EDI's announcement as well.

The guards opened fire, forcing Shepard and her team to take cover behind the lab tables and return fire. Shepard took several hits, but her shields managed to absorb the blows while she took down one of the guards with several bursts from her Battle Rifle.

"It appears from internal communications traffic that Doctor Kelaar has taken control of the station." EDI continued as Shepard took cover behind a now toppled lab table to eject her thermal clip.

Shepard cursed quietly. This was a rebellion of some type. Either Kelaar didn't like Cerberus or – more likely – he was power-hungry.

Glancing to her left, Shepard saw Jack smashing a guard into the wall repeatedly with a biotic shockwave, rendering him out of the fight.

To Shepard's right, Miranda used biotics to pull one of the guards towards her and took him out with a few well placed shots from her hand cannon.

A yellow-orange sphere whizzed past as Tali's drone raced across the room and stunned the two guards nearest to the door. A few well placed bursts and the guards knew no more as Miranda, Jack, and Shepard cornered and obliterated the final guard with a combination of biotics and shotgun fire.

When all of the combat was over and the room was silent once more, Shepard stood.

"Dumbasses…" Jack spoke up. "They didn't even take cover. Did they really think we'd go down that easily?"

"It doesn't matter at this point," Shepard responded, moving to take the guards spare thermal clips. "Kelaar has taken control of the station. We have to assume all guards are hostile."

"Shepard, you may want to come and look at this." Tali's voice came from one corner of the room.

Shepard, Jack, and Miranda approached Tali, who was sitting in a chair and gesturing to the computer positioned on the desk. The screen displayed several files.

"What's this?" Shepard asked. She wasn't a tech expert like Tali was.

"These are a series of videos from Doctor Kelaar. Something like a video diary," The quarian responded, bringing up the display on a larger monitor positioned near the ceiling for the others' convenience. "Most of them have something to do with either a 'Project Crimson' or a 'Subject Crimson'."

Miranda furrowed her eyebrows. She approached the computer and replaced Tali in the chair, taking a closer look at some of the file names.

"What's up, Miranda?" Shepard said, glancing at the door and wondering why nobody had rushed in to investigate what the ruckus was.

"These logs may reveal something about what happened here. We should watch some of them. But the file names are… well I hope they're wrong." Miranda merely said cryptically, initiating playback of one of the videos.

An image of Doctor Kelaar appeared on screen.

"Day fourteen," He began. "I've decided to call the boy 'Subject Crimson' due to the project name. I can't believe that Miranda merely wanted to aid his recovery! The boy is… unique. I've done several scans already; he recovered from the implantation process within only a few days." He said. He seemed breathless in his apparent excitement.

"His regeneration rate is absolutely astounding! I cut his arm open with a scalpel and it healed in just a few minutes! I'm going to have to do some more tests…"

The video ended and Miranda started playing another.

"Day forty-seven. After extensive experimentation, I've determined that Miranda was right when she said that Subject Crimson had three different energy sources. The potential he holds is amazing! If we could isolate the energy that gives him such high regeneration we could implant it into other humans and apply the same effect to them. However, it does pose a problem. Whenever I cut the boy open to get at his internal organs he begins healing so fast that I only have a few hours at best before the energy starts lashing out—it seems very similar to biotic energy, and the readings we're getting are phenomenal! It's almost like it has a mind of its own, defending its host from further harm. It's very fascinating, but problematic."

"The Illusive Man has been inquiring about the progress of Project Crimson. I don't think that he would quite… appreciate my experimentation, so I've sent some false information."

The video ended.

"He was cutting the boy open?" Miranda murmured to herself with something similar to disgust. Shepard remained silent. Miranda began to play another video.

"Day ninety-three. Subject Crimson has started responding to my tests. They're very minor reactions, a twitch of the finger here, a wince there, but it shows that he may be somewhat conscious during my experimentation. I'll have to be careful, I don't want him waking up in the middle of an experiment due to the pain; I might accidentally kill him." Kelaar said with a chuckle.

"Miss Addler is still a problem, though. It appears she has become attached to the boy, and refuses to help with my experimentation. She says that it's 'wrong'. It doesn't matter anyway, I'll be getting my own medical staff soon, and I've ensured they'll have no complaints about my… unorthodox methods of experimentation. There won't be nearly as many of them, but they'll do."

The video ended.

"This 'Doctor Kelaar' doesn't seem to have many morals." Shepard stated. Tali and Miranda nodded, while Jack stayed silent and watched the monitor intently when Miranda began playing another video.

"Day one-hundred-forty-two. Subject Crimson's energies are increasing. I have no idea how, but his potential keeps growing and growing. Recent scans have shown that the neural and skeletal implants in his system are… _absorbing_ his energy. I'm not entirely sure if it's a good or bad thing, only time will tell. His reactions are also getting more severe. He's kicked me a few times, and I think he grunted once, buy it may have just been a figment of my imagination."

"His regeneration speed is becoming greater and greater. Soon I may not be able to experiment on him at all; I'll have to work fast. I cut an inch-long gash into his stomach and it healed in a matter of hours! It's gotten to the point that I don't even need to stitch him up anymore, he heals on his own."

"Miss Addler has stopped coming to the office completely. She refuses to have anything to do with me and is calling me a monster," He chuckled as if the thought was unthinkable. "However, this may grow to be a major problem. She has started rallying some of the other personnel to her point of view. If this continues I may have a riot on my hands. I'll probably have to hire some better guards soon."

The video ended.

Shepard noticed that Jack was getting tense. Her fists were clenched and he looked about ready to punch a door in.

"You doing okay?" She questioned the convict, who seemed to relax a little at her words.

"I'll be fine, Shepard… This just reminds me too much of my own fucked up experience with Cerberus. At least _he_ wasn't conscious. The next time that bastard Kelaar sees me will be the last time he sees anything." She responded with venom.

With a nod from Shepard, Miranda began playing another video.

"Day two-hundred-nine," Kelaar looked different… and a little roughed up. He was excited, and he kept glancing behind him. A muffled shout could be heard through a door behind him.

"Subject Crimson has finally regained consciousness. I'm glad I've had the prudence to restrain him during my recent experiments. He woke just as I was removing his appendix. I must say, it amazes me how fast he regenerates at this point; last time it only took him three and a half days to re-grow it. It'll be interesting to see how fast it grows back now that he's conscious."

"I've sent my guards in to restrain him. He may not heal correctly if he keeps struggling against his restraints. On the bright side, I can do more extensive testing now that he's conscious. I'm going to start with his pain threshold and move on from there."

Another roar of rage from behind the door and a loud thud as something slammed against it, causing Kelaar to jump and the video to end.

Miranda was silent when the video turned to black and stared at the screen with wide eyes. Jack seemed once again ready to punch a door in and Tali was completely silent.

What the _hell_ was going on inside this station?

Miranda hesitated minutely before playing another video. Shepard wanted to tell her to stop – for all of their sakes – but her grim curiosity was too great.

"Day two-hundred-seventy-eight. I've been forced to place the civilian population into lockdown; Miss Addler was getting them too rowdy. They've all been placed under armed guard and will be confined to their quarters unless I need them. I've managed to acquire a sample of Subject Crimson's energy. It appears that the unknown energies are… merging with his biotic energy—their signatures are starting to overlap. Hopefully I'll be able to isolate the strain that causes his regeneration and find a way to implant it into other people before I lose it completely."

"Subject Crimson is starting to become a problem to contain. His strength is astounding, and it's only increasing—he threw one of my guards at least fifty feet a few days ago! I'll have to get better restraints; I'm not sure how long the current ones will hold him. I may have to start sending in other people to administer the sedatives; he's becoming too violent whenever I'm involved."

The video ended.

"Well, we know what happened to the crew. It also explains the lack of civilian personnel present when we were led through the station." Miranda stated after several seconds of silence.

Jack stayed silent and glared an imaginary hole into the monitor as Miranda started another video with a sense of dread.

"Day three-hundred-sixteen. There's no way that Subject Crimson was a civilian before we found him. Hell, he probably wasn't even normal military, his pain threshold is staggering. I actually burned the ends of his nerves off completely and he refused to cry out. They've since re-grown, so I'll have to try another method and hope I can get some decent data from that. I've been… training him, so to speak. I've been teaching him English – since he doesn't seem to know it, he's speaking some form of old Japanese – and I've had some of the crewmen give him lessons on how to use biotics. Nothing serious, just pushing blocks around and the like. It's amazing how fast he takes to it, he's a natural; I'll need to get biotic-resistant restraints soon."

"I've been forced to kill off most of the civilian population. Even under guard, they had the audacity to try and overthrow me! They call me a 'monster', but they don't understand anything! With the genetic data I'm getting from Subject Crimson I could make the human race more powerful biotically than even the asari and more invincible in battle than the krogan!"

"On another note, I think the Illusive Man's caught on to my experiments. I'm not entirely sure how; I think one of the civilians managed to get to the Comms Station and sent a message out, so I've disabled all outbound communications just in case. A recon team got here a few hours ago and I had them killed. I just hope the Illusive Man doesn't send anybody else… I can't afford to lose any more men if I want to start a coup d'état."

The video ended.

"I say we go take that motherfucker down right now," Jack said through clenched teeth.

"We should be careful about recruiting Subject Crimson, though. We can't be sure what state he's in at this point. He may not be mentally stable." Miranda said hesitantly.

"We should still give him a chance. Nobody deserves to go through something like that." Tali said quietly. It was hard to tell what emotions she was feeling due to her mask, but her body movements suggested something similar to pity.

Shepard nodded.

"EDI, download these files. We'll probably want to take a look at the rest of them later." Shepard said.

"Yes, Commander."

A muffled roar reached Shepard's ears. She glanced around and found the source to be one of the guards' helmets.

'_Must have been a something over the communications_.'

She removed the helmet and checked the communicator's frequency, dialing her own into that and prompting the other three to do so as well.

As soon as she did the sound of gunfire and panicked voices reached her ears.

"— _a hostile on sublevel four!"_

"_We have casualties on level three!"_

"_What the hell is going on here?"_

"_All personnel be on alert, Subject Crimson has gotten out of containment!"_

Shepard looked at the other three and gave them a nod, readying her rifle and exiting the room in full battle-mode, followed by the others. They snaked through the corridors towards the sounds of fighting, but encountered no resistance. Perhaps all of the guards had been called away?

As they approached a corner, the sounds of fighting grew much more prominent. They were getting close.

Shepard poked her head around the corner and drew it back just in time for an armored corpse to streak through the space her head had just occupied and smash into the wall behind them. The guard was obviously dead.

Shepard peered around the corner once again – a little more careful this time – and saw several guards backing slowly down the corridor towards them, firing wildly at a figure closing in on them.

The figure radiated a purple-ish color before emitting an animalistic roar, as well as a biotic pulse that tossed the group of guards about like ragdolls, slamming them into walls, ceilings, and floors alike.

The figure then ran to an intersection in the hallways and ran off to another section of the station.

"Well, I think we've found Subject Crimson." Shepard stated bluntly. She motioned for the other three to follow as she approached the intersection herself. The hallway had been severely damage, parts of the walls had been shredded, and burns from plasma shots were abundant. Several corpses lined the hallways as well.

She turned left at the intersection – the same direction Subject Crimson had went – and moved on.

~~PC~~

It had taken a while, but they had finally managed to track down Subject Crimson. The radio traffic helped a lot, as the guards frequently shouted their location when they saw him.

They ran around another corner to find him facing away from them, facing several guards who were firing wildly at him.

That seemed to be a pattern.

He was holding a slab of something – most likely metal – in front of him, which was taking most of the fire for him.

The shots that managed to hit him just bounced off of what appeared to be a biotic barrier and ricocheted into the walls. He thrust his hand out, clenched his fist and yanked it back, causing the guards in the back to be yanked towards him, bringing the rest of the guards with them in a heap.

He made a punching motion and a pulse of biotics emitted from his outstretched arm, sending the heap of guards tumbling down the corridor and into a wall. Several of them slammed into the corners of intersection with sickening cracks. None of them got up.

The young man discarded the now smoking piece of metal and cracked his neck.

Shepard and his team cautiously approached him from behind, Jack and Miranda already prepared to counter his biotics with their own.

He seemed to realize there was someone behind him and whipped around, his hands already charged with biotic energy. He stopped when he saw them though.

He was shirtless – most likely to make it easier for Kelaar to experiment on him – and wore a tattered pair of burnt orange pants. His dirtied blonde hair was vibrant, even with all of the grit it contained, and his chiseled face had an aura of power about it. The marks on his cheeks seemed to give him a feral look.

Shepard couldn't help but notice that he had a _very_ nice body.

"Who are you? You don't look like Cerberus…" He said more to himself than the four standing in front of him. Shepard shook herself from her thoughts.

"I'm Commander Shepard, and we're here to get you out of here." She said as calmly as she could while stepping forward.

"You… You're here to get me out?" He said, gazing at them with wary eyes. "Why should I believe you? For all I know, this is another of Kelaar's experiments." He questioned, the biotic energy flaring in his hands.

At this point Miranda stepped forward. The boy's eyes immediately focused on her… or rather, her uniform.

The one with the Cerberus insignia on it. The boy growled at them.

"So you _are_ Cerberus!" He shouted accusingly at them.

"I understand you're angry because of Doctor Kelaar, but—" Miranda began.

"You have _no fucking clue_ what that guy did to me." He cut her off.

Jack now stepped forward. Before she could speak, however, the boy raised an eyebrow and spoke, his demeanor suddenly much calmer.

"Well _you_ certainly don't look like the kind of person Cerberus would hire… And neither does the quarian, come to think of it, Cerberus is in the mindset that humans are the dominant species…" He said, adopting a thinking look.

Shepard raised an eyebrow. He wasn't really acting like the 'mentally unstable berserker' she had been expecting. She stepped forward once again, gaining the attention of the young man in front of her.

"Doctor Kellar wasn't acting under Cerberus orders. We found his video logs—we know about the 'experiments' Doctor Kelaar has been performing. Kelaar was planning to rebel against Cerberus and take charge himself."

The boy gave them another wary look. "That would explain the increase in guards… there are a lot more here than I thought there would be." He said, glancing at the large pile of bodies against the wall behind him. "Alright, I'll bite. You're here to get me out, what now?"

Miranda broke in once again. "_Now_ we need to get out of here. We can inform the Illusive Man about Kelaar's little rebellion and he'll handle it from there."

The boy immediately shook his head. "No deal," This caused Miranda to scowl at him. "I'm not leaving this station if Kelaar is still alive. You want me to come with you, Kelaar has to die. I'm not going to let anyone else be the subject of his 'experiments'." He said coldly.

Miranda looked to Shepard for the answer. She mulled it over for several seconds. The only way they could possible benefit from the mission was by convincing the boy to join them at this point. And from what she'd seen, he was every bit as powerful as the Illusive Man had made him out to be.

"Fine. We'll bring Doctor Kelaar to justice and then you'll come back to the Normandy with us. We'll go from there." Shepard responded with a nod.

The boy smiled. "So then, where to mister leader-man?" He said with a shit-eating grin.

Shepard gave him a somewhat surprised look. "I thought you would want to lead? Or are you going to charge off into the middle of things like you did earlier?"

The young man chuckled. "I don't think that's such a great idea. You're quarian friend probably isn't as durable as I am." He said, thumping his fist against his chest. "And I hate being the leader. If something goes wrong, everyone immediately assumes I fucked up." He said simply, shrugging.

Jack laughed. "You know, I think I'm going to like this guy." She said with a grin.

"Commander Shepard, I was able to triangulate Doctor Kelaar's current location from the communication's traffic. I'm sending you the navpoints now." EDI's voice echoed inside of Shepard's helmet.

"Thank you, EDI."

"If we're going to do this, we'd better get moving." Miranda stated.

Shepard nodded and the group of five readied their weapons – or in the boy's case, biotics – and proceeded down the halls.

~~PC~~

~A/N: Well, here it is, Chapter 2 of my Mass Effect/Naruto Crossover! Hope you all enjoyed the chap (or at least thought it was decent), but even if you didn't, click/tap/touch that review button and let me know! :P

Also, I haven't read/seen all of Naruto Shippuden (since I only watch the English dubbed anime xP), so if some of the history doesn't match up then that's why, and you'll just have to look past it.

_**Original Post ~ 7/22/2012 ~ 7,000 words**_


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